Organoid modeling of lung-intrinsic immune responses to SARS-CoV-2 infection

Current study of the mechanistic underpinnings of infectious disease is limited by an absence of human in vitro model systems which recapitulate the full spectrum of epithelial and immune responses induced by host-pathogen interactions. To address this gap, we describe a holistic, three-dimensional, air-liquid interface (ALI) lung organoid method from adult tissue comprising epithelial and stromal architecture along with a full complement of resident innate and adaptive immune cells. This novel system allows the study of the intrinsic tissue-resident immune function of the lung without requiring additional immune reconstitution from lung-extrinsic sources. Using SARS-CoV-2 infection of these 3D human lung ALI organoids, we demonstrate the ability of the endogenous immune system of the lung to mount a coordinated response including cytokine production, chemotaxis, adaptive CD4+ and CD8+ T-cell responses, and antibody production. Further, this immune response is dampened by inhibitors of viral replication and augmented in vaccinated individuals. Together, we describe the successful generation of human lung organoids that preserve the diversity of stromal and tissue-resident immune populations and SARS-CoV-2 infection thereof. This en bloc system demonstrates the sufficiency of lung to independently initiate anamnestic responses without a peripheral lymphoid component, as applicable to physiologic modeling of immune responses to SARS-CoV-2 and the broad study of pulmonary disease. Overall design: Organoids were harvested either from collagen or suspension, digested into single-cell suspensions, and sorted on a BD FACSAria II SORP for singlet discrimination, followed by live/dead gating, then CD45-/+gating, and analyzed using scRNAseq.